Please cite:
Schudoma et al.,
Nucl. Acids Res. 38: 970-980.
DOI 10.1093/nar/gkp1010.
'6-5-Internal Loop pdb3dllFX.n641-673
Source: [PDB-id:chain] 3dll:X (&rarr PDB)
Source: Information THE OXAZOLIDINONE ANTIBIOTICS PERTURB THE RIBOSOMAL PEPTIDYL-TRANSFERASE CENTER AND EFFECT TRNA POSITIONING
Source: Compound RRNA-23S RIBOSOMAL RNA
FLIPPED INTERNAL
Source: Resolution 3.50 ANGSTROMS.
Position (643, 671), (649, 664)
Primary structure ('_': anchors) _CGGAGG_-_UGAAA_
Bases with unusual sugar puckers
(Standard: C3'-endo) 		3: C4'-exo, 11: C2'-exo
Bases with unusual glycosidic-bond configuration
(Standard: anti) 		2: syn
Tertiary structure: Stacked bases
# Position 1 Position 2 Stacking direction
1 1 3 ↑
2 3 4 ↑
3 4 12 →
4 5 6 ↑
5 5 13 &larr
6 6 7 ↑
7 7 8 ↑
8 9 10 ↑
9 10 11 ↑
10 11 12 ↑
11 13 14 ↑
12 14 15 ↑
Tertiary structure: Base-pairs
(anchor pairs)
# Position 1 Position 2 Edges Configuration Single?
1 1 15 Watson-Crick/Watson-Crick cis
2 3 14 Watson-Crick/Watson-Crick cis
3 4 13 Hoogsteen/Sugar trans y
4 5 12 O2'/Bifurcated ?
5 5 13 Bifurcated/O2' ?
6 6 11 O2'/Bifurcated trans
7 6 12 Bifurcated/O2' ?
8 7 10 Watson-Crick/Watson-Crick cis y
9 8 9 Watson-Crick/Watson-Crick cis
Downloads Atom coordinates (PDB format)
Contact annotation (MC-Annotate format)
3D Structure Structure Graph
Structural Clusters